Fig. 1: Mouse atherosclerosis timecourse model and SMC cluster identity.

A Schematic of the single-cell RNA and ATAC sequencing data collection in the ApoE KO mouse atherosclerosis model. Created in BioRender. Li, D. (https://BioRender.com/22if1p3). Mice were tamoxifen gavaged at 8 weeks of age to induce Myh11-Cre recombination and tdTomato expression, single cells are isolated by flow cytometry and sorted on lineage traced and non-lineage traced cells. Mouse aortic root tissues were collected and scRNAseq assays performed on single cells isolated after 0, 3, 5, 7, 9, 12 or 16 weeks of high fat diet feeding. Remaining single cells from the same cellular samples underwent nuclei isolation and scATACseq assays at the 0-, 5-, 7-, 9-, 12-, and 16-week timepoints. (n = 23 scRNA libraries; n = 14 scATAC libraries, Supplementary Data 1). B UMAP embedding of all aortic root resident cells, with scRNAseq cluster assignment guided by cell-specific gene expression as we have described¹⁹. C UMAP of scRNA and scATAC clusters prior to integration. Confusion matrix showed cluster-cluster mapping between scRNA (x-axis) and scATAC (y-axis) cluster cell assignment data after CCA co-embedding. D UMAP visualization of the integrated object with scRNA and scATAC co-embedding. E–G Feature plots for specific marker genes Fbln1 (FMC-1), Fbln-2 (FMC-2), and Ibsp (CMC) in SMC. H–J Coverage plots of scATACseq open chromatin peaks for marker genes Fbln1, Fbln2, and Ibsp. K–M GSEA enrichment of cluster specific gene ontology biological process pathways for each modulated SMC cluster. N Representative slide image showing murine aorta tissue processed with Xenium Prime 5k gene expression panel. BCA – Brachiocephalic artery O Cropped image of ascending aorta with timecourse cell type labels transferred onto spatial data. P–S Image feature plot showing spatial distribution for specific marker genes Myh11 (SMC) Fbln1 (FMC-1), Fbln-2 (FMC-2), and Ibsp (CMC).